Fig. 3.

Characteristics and subclusters of mesenchymal cells in CSCC and CAde. (a–b) t-SNE plots of mesenchymal cells, colored by cell type and individual samples, respectively. (c) Dot plots presented the normalized expression levels of marker genes in identified mesenchymal subclusters. (d) Four fibroblastic subclusters were identified according to Pearson correlation coefficients based on GSEA results. (e) t-SNE plots of fibroblasts colored by cell types (upper) and expression of canonic genes (lower), respectively. (f) Dot plots displayed the GO enrichment terms of four fibroblastic subclusters. (g) Box plot displayed the composition comparison for four fibroblastic subclusters in CSCC and CAde. The P-values were calculated by Wilcoxon Rank Sum Test. (h–i) Developmental trajectory of fibroblasts constructed by monocle 2, colored by pseudo-time and pathologic types, respectively. (j) Pseudo-time heatmap displayed the genes involved in the developmental process of fibroblasts (left), and the enrichment GO terms of gene sets of different fibroblastic subclusters were also displayed (right). (k) Pseudo-time heatmap displayed dynamic changes of some representative TFs involved in the developmental process of fibroblasts.